Rwanda was the first low-income African country to introduce RotaTeq vaccine into its Expanded Programme on Immunization in May 2012. To gain insights into the overall genetic make-up and evolution of Rwandan G1P[8] strains pre- and... more
Rwanda was the first low-income African country to introduce RotaTeq vaccine into its Expanded Programme on Immunization in May 2012. To gain insights into the overall genetic make-up and evolution of Rwandan G1P[8] strains pre- and post-vaccine introduction, rotavirus positive fecal samples collected between 2011 and 2016 from children under the age of 5 years as part of ongoing surveillance were genotyped with conventional RT-PCR based methods and whole genome sequenced using the Illumina MiSeq platform. From a pool of samples sequenced (n = 158), 36 were identified as G1P[8] strains (10 pre-vaccine and 26 post-vaccine), of which 35 exhibited a typical Wa-like genome constellation. However, one post vaccine strain, RVA/Human-wt/RWA/UFS-NGS:MRC-DPRU442/2012/G1P[8], exhibited a RotaTeq vaccine strain constellation of G1-P[8]-I2-R2-C2-M2-A3-N2-T6-E2-H3, with most of the gene segments having a close relationship with a vaccine derived reassortant strain, previously reported in USA in ...
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Reviews of the global distribution of rotavirus genotypes have revealed the continuous circulation of G8 strains in Africa, often responsible for more cases of rotavirus disease than the more common G1-G4 rotavirus strains. During the... more
Reviews of the global distribution of rotavirus genotypes have revealed the continuous circulation of G8 strains in Africa, often responsible for more cases of rotavirus disease than the more common G1-G4 rotavirus strains. During the study, genotype G8 strains from Malawi, Kenya, and South Africa were detected and the VP7 and VP4 genes of selected specimens were sequenced. Results indicated that G8 strains appeared to reassort frequently and were associated with P[6], P[4], and P[8] specificity. Phylogenetic analysis suggested that G8 strains occurred in a North/South African phylogenetic divide. In addition, G8 strains appear to be able to infect non-human primates and strains with close phylogenetic relationships were detected in the same year on two continents. Any rotavirus vaccine introduced into African environments will need to demonstrate protective efficacy against unusual genotype combinations, new serotypes, and animal strains. Therefore, continuous monitoring of rotavirus strains in human and animal populations in Africa is a necessity.
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Genotyping of human rotaviruses was performed on 312 rotavirus-positive samples collected from 2,205 young children with diarrhea in the Upper East District of Ghana, a rural community. Of the 271 (86.9%) rotavirus strains that could be... more
Genotyping of human rotaviruses was performed on 312 rotavirus-positive samples collected from 2,205 young children with diarrhea in the Upper East District of Ghana, a rural community. Of the 271 (86.9%) rotavirus strains that could be VP7 (G) or VP4 (P) characterized, 73 (26.9%) were of G9 specificity. The predominant G9 genotype was G9P[8], which constituted 79.5% of all G9 strains detected, followed by G9P[6] (12.3%), G9P[10] (2.7%), and G9P[4] (1.3%). G9 strains with mixed P types constituted 2.7% of all G9 strains found in the study. All the G9P[8] strains had a long RNA electrophoretic pattern with VP6 subgroup II specificity. Four G9 isolates, GH1319, GH1416, GH3550, and GH3574, which were selected based on the abundance of stool material and were representative of the three electropherotypes observed, were cloned and sequenced. The Ghanaian isolates shared more than 98% sequence nucleotide homology with other G9 strains from the United States (US1205), Malawi (MW69), Brazil...
Research Interests: Biology, Ghana, Medicine, Molecular Epidemiology, Clinical Microbiology, and 15 moreDiarrhea, Biological Sciences, Phylogeny, Humans, Clinical, Infant, Phylogenetic analysis, Newborn Infant, Rotavirus, Genotype, Nucleotides, Nino, Molecular Sequence Data, Child preschool, and Medical and Health Sciences
Animal-human interspecies transmission is thought to play a significant role in influencing rotavirus strain diversity in humans. Proving this concept requires a better understanding of the complete genetic constellation of rotaviruses... more
Animal-human interspecies transmission is thought to play a significant role in influencing rotavirus strain diversity in humans. Proving this concept requires a better understanding of the complete genetic constellation of rotaviruses circulating in various animal species. However, very few whole genomes of animal rotaviruses, especially in developing countries, are available. In this study, complete genetic configuration of the first African camel rotavirus strain (RVA/Camel-wt/SDN/MRC-DPRU447/2002/G8P[11]) was assigned a unique G8-P[11]-I2-R2-C2-M2-A18-N2-T6-E2-H3 genotype constellation that has not been reported in other ruminants. It contained a novel NSP1 genotype (genotype A18). The evolutionary dynamics of the genome segments of strain MRC-DPRU447 were rather complex compared to those found in other camelids. Its genome segments 1, 3, 7-10 were closely related (>93% nucleotide identity) to those of human-animal reassortant strains like RVA/Human-tc/ITA/PA169/1988/G6P[14] and RVA/Human-wt/HUN/Hun5/1997/G6P[14], segments 4, 6 and 11 shared common ancestry (>95% nucleotide identity) with bovine rotaviruses like strains RVA/Cow-wt/CHN/DQ-75/2008/G10P[11] and RVA/Cow-wt/KOR/KJ19-2/XXXX/G6P[7], whereas segment 2 was closely related (94% nucleotide identity) to guanaco rotavirus strain RVA/Guanaco-wt/ARG/Rio_Negro/1998/G8P[1]. Its genetic backbone consisted of DS-1-like, AU-1-like, artiodactyl-like and a novel A18 genotype. This suggests that strain MRC-DPRU447 potentially emerged through multiple reassortment events between several mammalian rotaviruses of at least two genogroups or simply strain MRC-DPRU447 display a unique progenitor genotypes. Close relationship between some of the genome segments of strain MRC-DPRU447 to human rotaviruses suggests previous occurrence of reassortment processes combined with interspecies transmission between humans and camels. The whole genome data for strain MRC-DPRU447 adds to the much needed animal rotavirus data from Africa which is limited at the moment.
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Rotavirus is the major viral cause of diarrhoea in children worldwide. In this study, the first from Cameroon, the molecular epidemiology of rotavirus infection was investigated. Eight hundred and ninety diarrhoea stools collected from... more
Rotavirus is the major viral cause of diarrhoea in children worldwide. In this study, the first from Cameroon, the molecular epidemiology of rotavirus infection was investigated. Eight hundred and ninety diarrhoea stools collected from children under the age of 5 years in Western Cameroon between 1999 and 2000 were analysed for rotaviruses and further characterized by antigenic and genomic methods. Rotaviruses were detected in 21.9 per cent of stools and were highest during the cool dry season. Sixteen different electrophoretic patterns, 13 of long and three of short, were detected in the study area. The predominant subgroup detected was subgroup II (66.9 per cent) and atypical strains with long electropherotype, but subgroup I specificity were also observed. Rotavirus infection was shown to be an important component of diarrhoeal disease in young children in Cameroon. The results of this study in Cameroon reinforces the need to continue with surveillance programmes in Africa.
Research Interests: Microbiology, Medical Microbiology, Cameroon, Adolescent, Molecular Epidemiology, and 15 moreDiarrhea, Humans, Child, Female, Male, Gastroenteritis, Infant, Rotavirus, Medical virology, Feces, Enzyme Linked Immunosorbent Assay, Medical, Child preschool, Paediatrics and reproductive medicine, and Cross Infection
BackgroundGastroenteritis is a public health concern due to high morbidity and mortality among children. Rotaviruses are the leading etiological agents of severe gastroenteritis in children and accounts for more than half a million deaths... more
BackgroundGastroenteritis is a public health concern due to high morbidity and mortality among children. Rotaviruses are the leading etiological agents of severe gastroenteritis in children and accounts for more than half a million deaths per year in Africa. The study aimed at investigating the rotavirus genotypes that were circulating in children aged 5 years and below in and around Mukuru slums in Nairobi County Kenya.MethodsA purposive cross sectional sampling method was applied where 166 samples were collected from children below 5 years of age and taken to Kenya Medical Research Institute virology laboratory. Presence of rotaviruses was determined using reverse transcription polymerase chain reaction, while extraction was done using ZR Soil/Fecal RNA MicroPrep™ extraction kit. This was followed by reverse transcription and genotyping using various group A rotavirus primers.ResultsThe G type was successfully determined in 37 (92.5%), while the P type was successfully determined ...
Research Interests: Kenya, Humans, Female, Male, Gastroenteritis, and 5 moreInfant, Rotavirus, Feces, Cross Sectional Studies, and Child preschool
Human respiratory syncytial virus (HRSV) is a leading cause of acute respiratory illness in young children worldwide. Whole genome sequencing of HRSV offers enhanced resolution of strain variability for epidemiological surveillance and... more
Human respiratory syncytial virus (HRSV) is a leading cause of acute respiratory illness in young children worldwide. Whole genome sequencing of HRSV offers enhanced resolution of strain variability for epidemiological surveillance and provides genomic information essential for antiviral and vaccine development. A 10-amplicon one-step RT-PCR assay and a 20-amplicon nested RT-PCR assay with enhanced sensitivity were developed to amplify whole HRSV genomes from samples containing high and low viral loads, respectively. Ninety-six HRSV-positive samples comprised of 58 clinical specimens and 38 virus isolates with Ct values ≤ 24 were amplified successfully using the 10-amplicon one-step RT-PCR method and multiplexed in a single MiSeq run. Genome coverage exceeded 99.3% for all 96 samples. The 20-amplicon nested RT-PCR NGS method was used to generate >99.6% HRSV full-length genome for 72 clinical specimens with Ct values ranging from 24 to 33. Phylogenetic analysis of the genome sequences obtained from the 130 clinical specimens revealed a wide diversity of HRSV genotypes demonstrating methodologic robustness.
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Rotavirus is responsible for 26% of diarrheal deaths in Latin America and the Caribbean. Haiti introduced the monovalent rotavirus vaccine in April 2014. The objective of this analysis is to describe the impact of the rotavirus vaccine on... more
Rotavirus is responsible for 26% of diarrheal deaths in Latin America and the Caribbean. Haiti introduced the monovalent rotavirus vaccine in April 2014. The objective of this analysis is to describe the impact of the rotavirus vaccine on hospitalizations among Haitian children younger than 5 years old during the first 5 years after introduction. This analysis includes all children with diarrhea who were enrolled as part of a sentinel surveillance system at two hospitals from May 2013 to April 2019. We compare the proportion of rotavirus-positive specimens in each post-vaccine introduction year to the pre-vaccine period. To account for the potential dilution of the proportion of rotavirus-positive specimens from a waning cholera outbreak, we also analyzed annual trends in the absolute number of positive stools, fit a two-component finite-mixture model to the negative specimens, and fit a negative binomial time series model to the pre-vaccine rotavirus-positive specimens to predict t...
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A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and... more
A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 is often observed in porcine strains. Phylogenetic analyses showed that VP6, VP7, NSP2, NSP4, and NSP5 genes were closely related to cognate gene sequences of porcine strains (e.g., RVA/Pig-wt/CHN/DZ-2/2013/G5P[X] for VP7) from the NCBI database, while VP1, VP3, VP4, and NSP3 were closely related to porcine-like human strains (e.g., RVA/Human-wt/CHN/E931/2008/G4P[6] for VP1, and VP3). On the other hand, the origin of the VP2 was not clear from our analyses, as it was not only close to both porcine (e.g., RVA/Pig-tc/CHN/SWU-1C/2018/G9P[13]) and porcine-like human strains (e.g., RVA/Human-wt/LKA/R1207/2009/G4P[6]) but also ...
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Rotavirus G1P[8] strains account for more than half of the group A rotavirus (RVA) infections in children under five years of age, globally. A total of 103 stool samples previously characterized as G1P[8] and collected seven years before... more
Rotavirus G1P[8] strains account for more than half of the group A rotavirus (RVA) infections in children under five years of age, globally. A total of 103 stool samples previously characterized as G1P[8] and collected seven years before and seven years after introducing the Rotarix® vaccine in South Africa were processed for whole-genome sequencing. All the strains analyzed had a Wa-like constellation (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). South African pre- and post-vaccine G1 strains were clustered in G1 lineage-I and II while the majority (84.2%) of the P[8] strains were grouped in P[8] lineage-III. Several amino acid sites across ten gene segments with the exception of VP7 were under positive selective pressure. Except for the N147D substitution in the antigenic site of eight post-vaccine G1 strains when compared to both Rotarix® and pre-vaccine strains, most of the amino acid substitutions in the antigenic regions of post-vaccine G1P[8] strains were already present during the p...
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Rotavirus is the leading global cause of diarrheal mortality for unvaccinated children under five years of age. The outer capsid of rotavirus virions consists of VP7 and VP4 proteins, which determine viral G and P types, respectively, and... more
Rotavirus is the leading global cause of diarrheal mortality for unvaccinated children under five years of age. The outer capsid of rotavirus virions consists of VP7 and VP4 proteins, which determine viral G and P types, respectively, and are primary targets of neutralizing antibodies. Successful vaccination depends upon generating broadly protective immune responses following exposure to rotaviruses presenting a limited number of G and P type antigens. Vaccine introduction resulted in decreased rotavirus disease burden but also coincided with emergence of uncommon G and P genotypes, including G12. To gain insight into the recent predominance of G12P[8] rotaviruses in the U.S., we evaluated 142 complete rotavirus genome sequences and metadata from 151 clinical specimens collected in Nashville, TN from 2011-2013 through the New Vaccine Surveillance Network. Circulating G12P[8] strains were found to share many segments with other locally circulating strains but to have distinct conste...
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Rotavirus gastroenteritis is a major cause of death among children under 5 years globally. A rotavirus gastroenteritis surveillance program started in October 2011 in the Central African Republic (CAR) with the Surveillance... more
Rotavirus gastroenteritis is a major cause of death among children under 5 years globally. A rotavirus gastroenteritis surveillance program started in October 2011 in the Central African Republic (CAR) with the Surveillance Epidémiologique en Afrique Centrale (SURVAC) project. We present here genotyping results showing the emergence of G9 and G12 genotypes in Central African Republic. Among 222 children hospitalized with acute gastroenteritis who had a stool sample collected at the sentinel site, Complexe Pédiatrique de Bangui (CPB), Bangui, Central African Republic, 100 (45%) were positive for rotavirus between January 2014 and February 2016. During this period the most common rotavirus strains were G1P[8] (37%), G12P[6] (27%) and G9P[8] (18%).
The aim of this review was to assess all the studies on rotavirus G and P characterization during the pre-vaccine period (1999-2013) in Cameroon to have a better basis for post-vaccine introduction evaluations. A retrospective study was... more
The aim of this review was to assess all the studies on rotavirus G and P characterization during the pre-vaccine period (1999-2013) in Cameroon to have a better basis for post-vaccine introduction evaluations. A retrospective study was done through a comprehensive review of published (PubMed, Google Scholar) and accessible unpublished data on rotavirus G and P genotypes circulating in five regions of Cameroon. Descriptive data were expressed as frequencies tables and proportions. A total of 1844 rotavirus positive cases were analyzed. In all, 1534 strains were characterized for the P (VP4) specificity. Six different VP4 genotypes were observed, including P [4], P [6], P [8], P [9], P [10] and P [14]. The most predominant P genotypes were P [8] at 42.6%, and P [6] at 37.9%. Mixed infections were observed at 5.3%, whereas 4.1% of the strains were P non-typeable. A total of 1518 rotavirus strains were characterized for the G (VP7) specificity. VP7 genotypes G1, G2, G3, G4, G5, G6, G8,...
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Although first detected in animals, the rare rotavirus strain G10P[14] has been sporadically detected in humans in Slovenia, Thailand, United Kingdom and Australia among other countries. Earlier studies suggest that the strains found in... more
Although first detected in animals, the rare rotavirus strain G10P[14] has been sporadically detected in humans in Slovenia, Thailand, United Kingdom and Australia among other countries. Earlier studies suggest that the strains found in humans resulted from interspecies transmission and reassortment between human and bovine rotavirus strains. In this study, a G10P[14] rotavirus genotype detected in a human stool sample in Honduras during the 2010-2011 rotavirus season, from an unvaccinated 30-month old boy who reported at the hospital with severe diarrhea and vomiting, was characterised to determine the possible evolutionary origin of the rare strain. For the sample detected as G10P[14], 10% suspension was prepared and used for RNA extraction and sequence independent amplification. The amplicons were sequenced by next-generation sequencing using the Illumina MiSeq 150 paired end method. The sequence reads were analysed using CLC Genomics Workbench 6.0 and phylogenetic trees were con...
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AbstractRotavirus commonly causes diarrhea in children, leading to hospitalization and even death. Rapid diagnostic tests are feasible alternatives for determining rotavirus outbreaks in refugee camps that have inadequate laboratory... more
AbstractRotavirus commonly causes diarrhea in children, leading to hospitalization and even death. Rapid diagnostic tests are feasible alternatives for determining rotavirus outbreaks in refugee camps that have inadequate laboratory capacity. We evaluated the field performance of ImmunoCard STAT!(®) Rotavirus (ICS-RV) in Dadaab Refugee Camp and at the Kenya-Somalia border. From May to December 2014, we prospectively enrolled children aged < 5 years hospitalized with acute diarrhea, defined as ≥ 3 episodes of loose stool in 24 hours for < 7 days. Stool samples were collected and tested by trained surveillance clerks using ICS-RV per manufacturer's instructions. The field performance characteristics of ICS-RV were evaluated against the gold standard test, Premier(™) Rotaclone(®) enzyme immunoassay. The operational characteristics were evaluated using World Health Organization (WHO) ASSURED criteria to determine whether ICS-RV is appropriate as a point-of-care test by adminis...
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We report the genome of a novel human triple-recombinant G4P[6-8_R] mono-reassortant strain identified in a stool sample from the Dominican Republic during routine facility based rotavirus strain surveillance. The strain was designated as... more
We report the genome of a novel human triple-recombinant G4P[6-8_R] mono-reassortant strain identified in a stool sample from the Dominican Republic during routine facility based rotavirus strain surveillance. The strain was designated as RVA/Human-wt/DOM/2013840364/2013/G4P[6-8_R], with a genomic constellation of G4-P[6-8_R]-I1-R1-C1-M1-(A1-A8_R)-N1-(T1-T7_R)-E1-H1. Recombinant gene segments NSP1 and NSP3, were generated as a result of recombination between genogroup 1 rotavirus A1 human strain and a genotype A8 porcine strain and between genogroup 1 rotavirus T1 human strain and a genotype T7 bovine strain, respectively. Analyses of the RNA secondary structures of gene segment VP4, NSP1 and NSP3 showed that, all the recombinant regions appear to start in a loop (single stranded) region and terminated in a stem (double stranded) structure. Also, the VP7 gene occupied lineage VII within the G4 genotypes consisting of mostly porcine or porcine-like G4 strains, suggesting the occurren...
Research Interests: Genomics, Molecular Evolution, Biology, Medicine, Dominican Republic, and 15 moreBiological Sciences, Phylogeny, Humans, Animals, Gastroenteritis, Molecular Phylogenetics and Evolution, Cattle, Rotavirus, Genotype, Feces, Genetic Recombination, Genetic variation, Nucleic Acid Conformation, Medical and Health Sciences, and Epidemiological monitoring
Techniques such as the real-time reverse transcription-polymerase chain reaction (qRT-PCR) can detect RNA in samples with a low viral load. However, these amplicons typically are either too short or at insufficient concentrations for use... more
Techniques such as the real-time reverse transcription-polymerase chain reaction (qRT-PCR) can detect RNA in samples with a low viral load. However, these amplicons typically are either too short or at insufficient concentrations for use in subsequent sequencing reactions for genotyping and detection confirmation. The assay developed in this study detects rotavirus G genotypes and P genotypes with viral loads as low as 6.2 and 8.2 copies per reaction, respectively. The assay was validated using a panel of 91 stool samples, 32 reference rotavirus strains, and 6 non-target enteric virus samples.
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Group A rotaviruses (RVA) are a significant cause of pediatric gastroenteritis worldwide. The New Vaccine Surveillance Network (NVSN) has conducted active surveillance for RVA at pediatric hospitals and emergency departments at three to... more
Group A rotaviruses (RVA) are a significant cause of pediatric gastroenteritis worldwide. The New Vaccine Surveillance Network (NVSN) has conducted active surveillance for RVA at pediatric hospitals and emergency departments at three to seven geographically diverse sites in the U.S. since 2006. Over six consecutive years, from 2008 to 2013, 1,523 samples from NVSN sites that were test-positive by Rotaclone® enzyme immunoassay were submitted to the CDC for genotyping. In the 2009, 2010, and 2011 seasons, genotype G3P[8] was the predominant genotype throughout the network with 46-84% prevalence. In the 2012 season, G12P[8] replaced G3P[8] as the most common genotype with 70% prevalence and this trend persisted in 2013 (68.0% prevalence). Vaccine (RotaTeq®, Rotarix®) strains were detected in 0.6-3.4% of genotyped samples each season. Uncommon and unusual strains (e.g., G8P[4], G3P[24], G2P[8], G3P[4], G3P[6], G24P[14], G4P[6], G9P[4]) were detected sporadically over the study period...
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Background.Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA... more
Background.Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time.Methods.In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR...
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The goal of the SURVAC pilot project was to strengthen disease surveillance and response in three countries; Cameroon (CAE), Democratic Republic of the Congo (DRC) and Central African Republic (CAR). Seven laboratories involved in... more
The goal of the SURVAC pilot project was to strengthen disease surveillance and response in three countries; Cameroon (CAE), Democratic Republic of the Congo (DRC) and Central African Republic (CAR). Seven laboratories involved in rotavirus surveillance were provided with equipment, reagents and supplies. CDC and WHO staff provided on-site classroom and bench training in biosafety, quality assurance, quality control (QC), rotavirus diagnosis using Enzyme Immunoassay (EIA), and genotyping of rotavirus strains using the Reverse-Transcription Polymerase chain reaction (RT-PCR). All laboratory data were reported through WHO/AFRO. 23 staff members were trained on RT-PCR for rotavirus genotyping which was introduced for the first time in all three countries. In CAE, the number of samples analyzed by EIA and RT-PCR increased tenfold between 2007 and 2013. In DRC, this number increased fivefold, from 2009 to 2013 whereas in CAR, it increased fourfold between 2011 and 2013. All laboratories ...
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Using a multi-center, active surveillance network from two rotavirus seasons (2012 and 2013), we assessed the vaccine effectiveness of RV5 (RotaTeq) and RV1 (Rotarix) rotavirus vaccines in preventing rotavirus gastroenteritis... more
Using a multi-center, active surveillance network from two rotavirus seasons (2012 and 2013), we assessed the vaccine effectiveness of RV5 (RotaTeq) and RV1 (Rotarix) rotavirus vaccines in preventing rotavirus gastroenteritis hospitalizations and emergency department (ED) visits for numerous demographic and secular strata. We enrolled children hospitalized or visiting the ED with acute gastroenteritis (AGE) for the 2012 and 2013 seasons at 7 medical institutions. Stool specimens were tested for rotavirus by enzyme immunoassay and genotyped, and rotavirus vaccination histories were compared for rotavirus-positive cases and rotavirus-negative AGE controls. We calculated the VE for preventing rotavirus associated hospitalizations and ED visits for each vaccine, stratified by vaccine dose, season, clinical setting, age, predominant genotype, and ethnicity. RV5-specific VE analyses included 2,961 subjects, 402 rotavirus cases (14%) and 2,559 rotavirus-negative AGE controls. RV1-specif...
Research Interests: Treatment Outcome, Biological Sciences, Emergency Medical Services, Humans, Child, and 13 moreHospitalization, United States, Female, Male, Gastroenteritis, Infant, Genotype, Feces, Enzyme Linked Immunosorbent Assay, Clinical Infectious Diseases, Child preschool, Medical and Health Sciences, and Epidemiological monitoring
The current two-step VP7 and VP4 genotyping RT-PCR assays for rotaviruses have been linked consistently to genotyping failure in an estimated 30% of RVA positive samples worldwide. We have developed a VP7 and VP4 multiplexed one-step... more
The current two-step VP7 and VP4 genotyping RT-PCR assays for rotaviruses have been linked consistently to genotyping failure in an estimated 30% of RVA positive samples worldwide. We have developed a VP7 and VP4 multiplexed one-step genotyping assays using updated primers generated from contemporary VP7 and VP4 sequences. To determine assay specificity and sensitivity, 17 reference virus strains, 6 non-target gastroenteritis viruses and 725 clinical samples carrying the most common VP7 (G1, G2, G3, G4, G9, and G12) and VP4 (P[4], P[6], P[8], P[9] and P[10]) genotypes were tested in this study. All reference RVA strain targets yielded amplicons of the expected sizes and non-target genotypes and gastroenteritis viruses were not detected by either assay. Out of the 725 clinical samples tested, the VP7 and VP4 assays were able to assigned specific genotypes to 711 (98.1%) and 714 (98.5%), respectively. The remaining unassigned samples were re-tested for RVA antigen using EIA and qRT-PCR assays and all were found to be negative. The overall specificity, sensitivity and limit of detection of the VP7 assay were in the ranges of 99.0-100%, 94.0-100% and 8.6×10(1) to 8.6×10(2) copies of RNA/reaction, respectively. For the VP4 assay, the overall specificity, sensitivity and limit of detection assay were in the ranges of 100%, 94.0-100% and ≤1 to 8.6×10(2) copies of RNA/reaction, respectively. Here we report two highly robust, accurate, efficient, affordable and documentable gel-based genotyping systems which are capable of genotyping 97.8% of the six common VP7 and 98.3% of the five common VP4 genotypes of RVA strains which are responsible for approximately 88.2% of all RVA infections worldwide.
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Group A rotaviruses are known to be major agents of severe acute gastroenteritis in infants and young animals worldwide. The possibility of interspecies transmission or genetic reassortant of rotavirus strains confirms that rotavirus... more
Group A rotaviruses are known to be major agents of severe acute gastroenteritis in infants and young animals worldwide. The possibility of interspecies transmission or genetic reassortant of rotavirus strains confirms that rotavirus remains a potential zoonotic infection and that animals could be reservoirs for human infection. 285 faecal samples from calves aged 0-6 months old (190 diarrheic and 95 non-diarrheic) were collected from settled and non-settled herds in Zaria. The samples were analysed using two commercially available ELISA kits. Kits for antigenic diagnosis of bovine rotavirus (RV) in cattle faeces (Bio-X Diagnostics, Belgium) and ProSpecT TM Rotavirus (Oxoid Ltd, UK) for the detection of Group A RV in human stool were used. Questionnaires were administered to obtain information on the herd and each calf sampled. Of the 285 faecal samples tested for group A RV antigen using both ELISA kits, 66 (23.16%) were positive. RV antigen was detected in 50 (26.32%) of the diarr...
Rotaviruses are known to be major cause of severe acute gastroenteritis in infants and young children worldwide. Three hundred and forty (340) diarrhoeic and 32 age matched control stool samples of children age 0-60 months were screened... more
Rotaviruses are known to be major cause of severe acute gastroenteritis in infants and young children worldwide. Three hundred and forty (340) diarrhoeic and 32 age matched control stool samples of children age 0-60 months were screened for the presence of rotavirus (RV) antigens using ELISA. During the study, 237 of the 372 children were being breastfed while 135 were not. Rotavirus was detected in 84 samples; 81(24%) from diarrhoeic children and 3 (9%) among the matched control children. Rotavirus was significantly associated with gastroenteritis (P = 0.006). Of the 84 positive cases, 48 (24%) were detected amongst 199 male patients while 36 (21%) were amongst 173 female children (P = 0.446). There was a significant association between RV infection and the age of the children studied (P = 0.014). The prevalence of infection decreased with increase in age with about 90% of the infection occurring among children 0-18 months of age and then peaked in children 0-6 months old. Breast f...
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Samples collected in 2012 through diarrheal disease surveillance in Haiti were tested for rotavirus by enzyme immunoassay and real time RT-PCR and positive samples were genotyped. The predominant genotypes were G1P[8] (29% prevalence) and... more
Samples collected in 2012 through diarrheal disease surveillance in Haiti were tested for rotavirus by enzyme immunoassay and real time RT-PCR and positive samples were genotyped. The predominant genotypes were G1P[8] (29% prevalence) and G9P[8] (21%). The observed genotype prevalence is similar to that reported previously for other Caribbean countries.
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We report the genomic characterization of a rare human G8P[14] rotavirus strain, identified in a stool sample from Guatemala (GTM) during routine rotavirus surveillance. This strain was designated as... more
We report the genomic characterization of a rare human G8P[14] rotavirus strain, identified in a stool sample from Guatemala (GTM) during routine rotavirus surveillance. This strain was designated as RVA/Human-wt/GTM/2009726790/2009/G8P[14], with a genomic constellation of G8-P[14]-I2-R2-C2-M2-A13-N2-T6-E2-H3. The VP4 gene occupied lineage VII within the P[14] genotype. Phylogenetic analysis of each genome segment revealed close relatedness to several zoonotic simian, guanaco and bovine strains. Our findings suggest that strain RVA/Human-wt/GTM/2009726790/2009/G8P[14] is an example of a direct zoonotic transmission event. The results of this study reinforce the potential role of interspecies transmission and reassortment in generating novel and rare rotavirus strains which infect humans.
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Research Interests: Biology, Medicine, Diarrhea, Biological Sciences, Disease Outbreaks, and 15 moreHumans, Female, Male, Gastroenteritis, Young Adult, Middle Aged, Rotavirus, Genotype, Adult, Feces, Clinical Infectious Diseases, Surveys and Questionnaires, Foodborne diseases, reverse transcriptase polymerase chain reaction, and Medical and Health Sciences
Introduction: Investigating the incidence and dynamics of HIV-2 and false-negative HIV test results in a highly sexually active population where frequent opportunities exist for acquiring and transmitting infections provides additional... more
Introduction: Investigating the incidence and dynamics of HIV-2 and false-negative HIV test results in a highly sexually active population where frequent opportunities exist for acquiring and transmitting infections provides additional understanding of the epidemiology of the virus in Africa. Methodology: The HIV status of 900 active female sex workers (FSWs) was determined using two lateral flow rapid assays in series. The second rapid test device incorporates type-specific recombinant peptides that discriminate between HIV-1 and HIV-2 infection. HIV sero-negative samples were re-tested for HIV infection and their viral loads determined using the NucliSENS real-time nucleic acid sequence-based amplification (NASBA) platform. Results: In total, 335 FSWs were determined to be HIV positive, the majority (227; 67.8%) of whom were between the ages of 20 and 30 years. Eighteen (5.4%) were found to have evidence of HIV-2 infection, 17 of whom were co-infected with HIV-1. Only one HIV-2 mo...
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Group A rotaviruses (RVA) are among the main global causes of severe diarrhea in children under the age of 5years. Strain diversity, mixed infections and untypeable RVA strains are frequently reported in Africa. We analysed... more
Group A rotaviruses (RVA) are among the main global causes of severe diarrhea in children under the age of 5years. Strain diversity, mixed infections and untypeable RVA strains are frequently reported in Africa. We analysed rotavirus-positive human stool samples (n=13) obtained from hospitalised children under the age of 5years who presented with acute gastroenteritis at sentinel hospital sites in six African countries, as well as bovine and porcine stool samples (n=1 each), to gain insights into rotavirus diversity and evolution. Polyacrylamide gel electrophoresis (PAGE) analysis and genotyping with G-(VP7) and P-specific (VP4) typing primers suggested that 13 of the 15 samples contained more than 11 segments and/or mixed G/P genotypes. Full-length amplicons for each segment were generated using RVA-specific primers and sequenced using the Ion Torrent and/or Illumina MiSeq next-generation sequencing platforms. Sequencing detected at least one segment in each sample for which duplicate sequences, often having distinct genotypes, existed. This supported and extended the PAGE and RT-PCR genotyping findings that suggested these samples were collected from individuals that had mixed rotavirus infections. The study reports the first porcine (MRC-DPRU1567) and bovine (MRC-DPRU3010) mixed infections. We also report a unique genome segment 9 (VP7), whose G9 genotype belongs to lineage VI and clusters with porcine reference strains. Previously, African G9 strains have all been in lineage III. Furthermore, additional RVA segments isolated from humans have a clear evolutionary relationship with porcine, bovine and ovine rotavirus sequences, indicating relatively recent interspecies transmission and reassortment. Thus, multiple RVA strains from sub-Saharan Africa are infecting mammalian hosts with unpredictable variations in their gene segment combinations. Whole-genome sequence analyses of mixed RVA strains underscore the considerable diversity of rotavirus sequences and genome segment combinations that result from a complex evolutionary history involving multiple host species.
Research Interests: Genetics, Biology, Medicine, Phylogeny, Humans, and 10 moreAnimals, Coinfection, Infant, Newborn Infant, Cattle, Rotavirus, Genotype, Swine, Animal Diseases, and Child preschool
The epidemiology of hepatitis C virus (HCV) infection has been partially described for at risk groups in urban communities in Nigeria. On the other hand, literature on the possible spread of the virus in rural Nigeria remains extremely... more
The epidemiology of hepatitis C virus (HCV) infection has been partially described for at risk groups in urban communities in Nigeria. On the other hand, literature on the possible spread of the virus in rural Nigeria remains extremely scanty. The objective of this study was to estimate the prevalence of HCV in a rural and urban community in Nigeria. Four hundred and twenty four (n = 424) plasma samples belonging to 238 rural inhabitants and 186 urban dwellers in North Central Nigeria were tested for anti-HCV markers using a third generation quantitative enzyme-linked immunosorbent assay (ELISA) that uses recombinant proteins and synthetic peptides derived from core and non-structural regions. 29(12.2%, CI = 0.17-0.86) of the rural samples and 5(2.7%, CI = 0.01-0.06) of urban samples were positive for HCV infection. The highest number of infections was in the 21-40 years age category. Our preliminary findings indicates that the number of HCV infection in rural was higher (p = 0.03) when compared with urban settings in Nigeria. Our results suggest a higher prevalence of HCV infection in rural than urban Nigeria in the region studied and possibly in Nigeria as a whole. HCV transmission is active in rural Nigeria and large scale studies to understand the dynamics of the infection are required so as to plan targeted preventive measures.
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Rotarix® and RotaTeq® vaccines have led to a dramatic reduction in rotavirus disease worldwide. However, the detection of porcine circovirus type 1 (PCV-1) and 2 (PCV-2) DNA in these vaccines raised some safety concerns. Studies examining... more
Rotarix® and RotaTeq® vaccines have led to a dramatic reduction in rotavirus disease worldwide. However, the detection of porcine circovirus type 1 (PCV-1) and 2 (PCV-2) DNA in these vaccines raised some safety concerns. Studies examining shedding of rotavirus in stool from rotavirus vaccine recipients have been performed but no published data exist regarding the shedding of PCV virus in stools of vaccinees. The goal of this study was to determine if PCV-1 and/or PCV-2 is shed in the feces of infants vaccinated with RotaTeq®. Using multiple PCR assays for detection of PCV DNA, we tested for PCV-1 and PCV-2 in 826 stool swab samples collected serially during the first 9 d after vaccination from 102 children vaccinated with RotaTeq®. Since the vaccine is recommended and uptake is high, we did not have samples from unvaccinated infants. A total of 235 (28.5%) samples from 59 vaccine recipients were positive for PCV-2 DNA by one or more assays used in this study. PCV-1 DNA was not detec...
Research Interests: Medicine, Humans, Female, Male, Polymerase Chain Reaction, and 4 moreInfant, Prevalence, Rotavirus, and Feces
Group A rotaviruses (RVA) are the leading cause of severe diarrhea in young children worldwide. Two live-attenuated RVA vaccines, Rotarix(®) and RotaTeq(®) are recommended by World Health Organization (WHO) for routine immunization of all... more
Group A rotaviruses (RVA) are the leading cause of severe diarrhea in young children worldwide. Two live-attenuated RVA vaccines, Rotarix(®) and RotaTeq(®) are recommended by World Health Organization (WHO) for routine immunization of all infants. Rotarix(®) and RotaTeq(®) vaccines have substantially reduced RVA associated mortality but occasionally have been associated with acute gastroenteritis (AGE) cases identified in vaccinees and their contacts. High-throughput assays are needed to monitor the prevalence of vaccine strains in AGE cases and emergence of new vaccine-derived strains following RVA vaccine introduction. In this study, we have developed quantitative real-time RT-PCR (qRT-PCR) assays for detection of Rotarix(®) and RotaTeq(®) vaccine components in stool samples. Real-time RT-PCR assays were designed for vaccine specific targets in the genomes of Rotarix(®) (NSP2, VP4) and RotaTeq(®) (VP6, VP3-WC3, VP3-human) and validated on sequence confirmed stool samples containin...
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This is a report of the complete genomic sequence of a rare rotavirus group A G3-P[9]-I2-R2-C2-M2-A3-N2-T1-E2-H3 strain designated RVA/Human-wt/USA/12US1134/2012/G3P[9].
Group A rotaviruses (RVA) are double stranded RNA viruses that are a significant cause of acute pediatric gastroenteritis. Beginning in 2006 and 2008, respectively, two vaccines, Rotarix™ and RotaTeq®, have been approved for use in the... more
Group A rotaviruses (RVA) are double stranded RNA viruses that are a significant cause of acute pediatric gastroenteritis. Beginning in 2006 and 2008, respectively, two vaccines, Rotarix™ and RotaTeq®, have been approved for use in the USA for prevention of RVA disease. The effects of possible vaccine pressure on currently circulating strains in the USA and their genome constellations are still under investigation. In this study we report 33 complete RVA genomes (ORF regions) collected in multiple cities across USA during 2006-2009, including 8 collected from children with verified receipt of 3 doses of rotavirus vaccine. The strains included 16 G1P[8], 10 G3P[8], and 7 G9P[8]. All 33 strains had a Wa like backbone with the consensus genotype constellation of G(1/3/9)-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. From maximum likelihood based phylogenetic analyses, we identified 3-7 allelic constellations grouped mostly by respective G types, suggesting a possible allelic segregation based on th...
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This is a report of the complete genomic sequence of a reassortant rotavirus group A G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2 strain designated RVA/Human-wt/USA/ LB1562/2010/G9P[4].
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The World Health Organization (WHO) recommends the introduction of rotavirus vaccine in the immunization program of all countries. In the Central African Republic (CAR), sentinel surveillance for rotavirus gastroenteritis was established... more
The World Health Organization (WHO) recommends the introduction of rotavirus vaccine in the immunization program of all countries. In the Central African Republic (CAR), sentinel surveillance for rotavirus gastroenteritis was established in 2011 by the Ministry of Health, with the support of the Surveillance en Afrique Centrale Project (SURVAC). The purpose of this study was to assess the burden of rotavirus gastroenteritis and to identify rotavirus strains circulating in CAR before the introduction of rotavirus vaccine planned for this year, 2014. One sentinel site and one laboratory at the national level were designated by the CAR Ministry of Health to participate in this surveillance system. Stool samples were collected from children who met the WHO rotavirus gastroenteritis case definition (WHO, 2006). The samples were first screened for group A rotavirus antigen by enzyme immunoassay (EIA), and genotyping assays performed using a multiplex reverse transcriptase PCR (RT-PCR) technique. Between October 2011 and September 2013, 438 stool samples were collected and analyzed for detection of rotavirus antigen; 206 (47%) were positive. Among the 160 (78%) that could be genotyped, G2P[6] was the predominant strain (47%) followed by G1P[8] (25%) and G2P[4] (13%). Almost half of stool samples obtained from children hospitalized with gastroenteritis were positive for rotavirus. These baseline rotavirus surveillance data will be useful to health authorities considering rotavirus vaccine introduction and for evaluating the efficacy of rotavirus vaccine once it is introduced into the routine immunization system.
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Rotavirus is the most common cause of severe diarrheal disease in children under 5 years of age worldwide. The World Health Organization (WHO) estimated that 453,000 rotavirus-attributable deaths occur annually. Through the WHO, the... more
Rotavirus is the most common cause of severe diarrheal disease in children under 5 years of age worldwide. The World Health Organization (WHO) estimated that 453,000 rotavirus-attributable deaths occur annually. Through the WHO, the Rotavirus Sentinel Surveillance Program was established in Cameroon in September 2007 with the Mother and Child Center (MCC) in Yaoundé playing the role of sentinel site and national laboratory for this program. The objectives of this surveillance were to assess the rotavirus disease burden and collect baseline information on rotavirus strains circulating in Cameroon. Diarrheal stool samples were collected in a pediatric hospital from children under 5, using the WHO case definition for rotavirus diarrhea. Antigen detection of rotavirus was performed by using an enzyme immunoassay (EIA). The genotypic characterization was performed using multiplexed semi-nested reverse transcription-polymerase chain reaction (RT-PCR) assays. Between September 2007 and December 2012, 2444 stool samples were received at the MCC laboratory for rotavirus antigen detection, of which 999 (41%) were EIA positive. Among EIA positive samples 898 were genotyped. Genotype prevalence varied each year. Genotype G9P[8] was the dominant type during 2007 (32%) and 2008 (24%), genotype G3P[6] predominated in 2010 (36%) and 2011 (25%), and G1P[8] was predominant in 2012 (44%). The findings showed that the rotavirus disease burden is high and there is a broad range of rotavirus strains circulating in Yaoundé. These data will help measure the impact of vaccination in the future.
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Over the past few years whole genome sequencing of rotaviruses has become a routine laboratory method in many strain surveillance studies. To study the molecular evolutionary pattern of representative Cameroonian Rotavirus A (RVA)... more
Over the past few years whole genome sequencing of rotaviruses has become a routine laboratory method in many strain surveillance studies. To study the molecular evolutionary pattern of representative Cameroonian Rotavirus A (RVA) strains, the semiconductor sequencing approach was used following random amplification of genomic RNA. In total, 31 RVA strains collected during 2010-2011 in three Cameroonian study sites located 120 to 1240 km from each other were sequenced and analyzed. Sequence analysis of the randomly selected representative strains showed that 18 RVAs were Wa-like, expressing G1P[6], G12P[6], or G12P[8] neutralization antigens on the genotype 1 genomic constellation (I1-R1-C1-M1-A1-N1-T1-E1-H1), whereas 13 other strains were DS-1-like, expressing G2P[4], G2P[6], G3P[6], and G6P[6] on the genotype 2 genomic constellation (I2-R2-C2-M2-A2-N2-T2-E2-H2). No inter-genogroup reassortment in the backbone genes was observed. Phylogenetic analysis of the Cameroonian G6P[6] stra...
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Group C rotavirus (GpC RV) is a causative agent of acute gastroenteritis in children and adults. We expressed the three major capsid proteins VP2, VP6 and VP7 of human GpC RV in baculovirus and demonstrated the self-assembly of VP2/6/7 or... more
Group C rotavirus (GpC RV) is a causative agent of acute gastroenteritis in children and adults. We expressed the three major capsid proteins VP2, VP6 and VP7 of human GpC RV in baculovirus and demonstrated the self-assembly of VP2/6/7 or VP6/7 virus-like particles (VLPs) in insect cells. We examined a number of parameters, including the kinetics of protein synthesis in different cell lines and media, to optimize the most favorable conditions for the synthesis of recombinant viral proteins and the production of VLPs in Sf9 cells. Hyperimmune serum to VP2/6/7 and VP6/7 VLPs recognized individual recombinant proteins of human GpC RV by Western blot analysis. This serum also showed specific reactivities with the corresponding GpC VLPs but not GpA RV by using immune electron microscopy (IEM) and enzyme immunoassay (EIA). The ability to produce an unlimited amount of GpC RV antigen and the availability of high quality antibody will allow us to develop sensitive and specific diagnostic assays to better determine the epidemiology and disease burden of GpC RV in humans.